Treatment of breast cancer

ABSTRACT

The disclosure provides methods for treating estrogen receptor positive (ER+) cancer in women, and in particular embodiments, methods for treating ER+ cancers having gain of function mutations in the ESR1 ligand binding domain, with an effective amount of a compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant, a pharmaceutically acceptable salt thereof, or a prodrug thereof. The disclosure also includes the detection of the Estrogen Receptor 1 (ESR1) gene mutations that lead to endocrine resistance and treatment of endocrine resistant ER+ cancers.

1. CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application Nos. 62/502,299, filed May 5, 2017; 62/457,759, filed Feb. 10, 2017; and 62/406,859, filed Oct. 11, 2016, each of which is incorporated in its entirety by reference.

2. SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Oct. 9, 2017, is named 38614PCT_CRF_sequencelisting.txt, and is 2,119 bytes in size.

3. BACKGROUND OF THE INVENTION

Estrogen receptor positive (ER⁺) breast cancers are a group of breast cancers that express estrogen receptor α (ERα). Approximately 70% of breast cancers are ER⁺ and are, therefore, treated with endocrine therapy. Endocrine therapy has led to significant improvement in outcome of women with ER⁺ breast cancer by lowering the level of estrogen or blocking estrogen signaling. However, its effectiveness is limited by intrinsic and acquired endocrine resistance.

Recent studies have shown evidence for the temporal selection of functional Estrogen Receptor 1 (ESR1) gene mutations as potential drivers of endocrine resistance during the progression of ER⁺ breast cancer. See Jeselsohn et al., Clinical Cancer Research 20(7): 1757-1767 (2014). The mutations in ESR1, the gene encoding ERα, change the conformation of the ERα protein, increase its interaction with its co-activators, promote an active form of the receptor in absence of hormone, and assist tumor cells in evading hormonal treatment. See Thomas and Gustafsson, Trends in Endocrinology and Metabolism 26(9): 467-476 (2015).

There thus remains a need to develop new therapeutic strategies that are effective to treat tumors harboring mutations in ESR1, and that can therefore be used to treat breast cancer patients who have developed endocrine resistance or who are at risk of developing endocrine resistance.

4. SUMMARY OF THE INVENTION

We engineered ERα expression constructs to express four ESR1 mutations in the ligand binding domain (LBD) of the ERα protein, Y537S, Y537N, Y537C, and D538G, and introduced these expression constructs into cells in culture. These mutations are found in ER⁺ metastatic breast cancer patients who have been treated with endocrine therapy. See Jeselsohn et al., Nature Reviews Clinical Oncology 12(10): 573-583 (2015); Jeselsohn et al., Clinical Cancer Research 20(7): 1757-1767 (2014); Robinson et al., Nature Genetics 45(12): 1446-1451(2013); Thomas and Gustafsson, Trends in Endocrinology and Metabolism 26(9): 467-476 (2015); and Toy et al., Nature Genetics 45(12): 1439-1445 (2013).

Using an estrogen receptor-responsive reporter construct, we confirmed in an ovarian cell line and in a breast cancer cell line that all mutants are constitutively active as compared to wild type ERα. We then treated the cells with raloxifene, bazedoxifene, tamoxifen, etacstil, or fulvestrant, and found that raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant each effectively inhibited the transcriptional activity of the ERα LBD mutants in a dose-response manner.

In a second series of experiments, we confirmed that tamoxifen and fulvestrant are able to reduce viability of the breast cancer cell line MCF7 stably transfected with either the Y537S or D538G ESR1 mutant receptor, at clinically achievable concentrations.

Accordingly, in a first aspect, a method of treating locally advanced or metastatic breast cancer in women is presented. The method comprises selecting for treatment a patient who has been diagnosed with estrogen receptor positive (ER⁺) locally advanced or metastatic breast cancer, and administering to the selected patient an effective amount of a compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant, a pharmaceutically acceptable salt thereof, or a prodrug thereof.

In various embodiments, the selected patient has previously been treated with one or more lines of endocrine therapy. In certain embodiments, the patient has previously been treated with a plurality of lines of endocrine therapy.

In some embodiments, the endocrine therapy that the patient has previously been treated with is a selective ER modulator (SERM). In some embodiments, the endocrine therapy that the patient has previously been treated with is a selective ER degrader (SERD).

In some embodiments, the endocrine therapy that the patient has previously been treated with is an aromatase inhibitor. In certain embodiments, the aromatase inhibitor is exemestane (Aromasin®), letrozole (Femara®), or anastrozole (Arimidex®).

In some embodiments, the patient has disease progression after endocrine therapy. In some embodiments, the patient is resistant to endocrine therapy.

In various embodiments, the patient's cancer has at least one gain of function missense mutation within the ligand binding domain (LBD) of the Estrogen Receptor 1 (ESR1) gene. In some embodiments, the patient has previously been determined to have at least one gain of function missense mutation within the ligand binding domain (LBD) of the Estrogen Receptor 1 (ESR1) gene. In certain embodiments, the method further comprises determining that the patient has at least one gain of function missense mutation within the ligand binding domain (LBD) of the Estrogen Receptor 1 (ESR1) gene.

In some embodiments, the at least one of gain of function missense mutation is in any one of amino acids D538, Y537, L536, P535, V534, S463, V392, or E380.

In certain embodiments, the at least one gain of function missense mutation is in the amino acid D538. In some preferred embodiments the mutation is D538G.

In certain embodiments, the at least one gain of function missense mutation is in the amino acid Y537. In some embodiments, the mutation is Y537S, Y537N, Y537C, or Y537Q. In some preferred embodiments, the mutation is Y537C.

In certain embodiments, the at least one gain of function missense mutation is in the amino acid L536. In some embodiments, the mutation is L536R or L536Q.

In certain embodiments, the at least one gain of function missense mutation is in the amino acid P535. In some embodiments, the mutation is P535H.

In certain embodiments, the at least one gain of function missense mutation is in the amino acid V534. In some embodiments, the mutation is V534E.

In certain embodiments, the at least one gain of function missense mutation is in the amino acid S463. In some embodiments, the mutation is S463P.

In certain embodiments, the at least one gain of function missense mutation is in the amino acid V392. In some embodiments, the mutation is V392I.

In certain embodiments, the at least one gain of function missense mutation is in the amino acid E380. In some embodiments, the mutation is E380Q.

In some embodiments, the serum estradiol level of the patient is at least 0.35 ng/dL. In some embodiments, the serum estradiol level of the patient is about 0.30 ng/dL to about 0.35 ng/dL. In yet some embodiments, the serum estradiol level of the patient is about 0.25 ng/dL to about 0.30 ng/dL.

In various embodiments, the compound is administered by oral, intravenous, transdermal, vaginal topical, or vaginal ring administration. In various embodiments, the compound is administered once every day, once every two days, once every three days, once every four days, once every five days, once every six days, once every week, once every two weeks, once every three weeks, or once every month.

In certain embodiments, the method further comprises treating the patient with at least one additional endocrine therapy. In some embodiments, the patient is treated with the additional endocrine therapy at original doses. In some other embodiments, the patient is treated with the additional endocrine therapy at doses higher than original doses. In certain embodiments, the additional endocrine therapy is treatment with lasofoxifene. In certain embodiments, the additional endocrine therapy is treatment with an aromatase inhibitor.

In various embodiments, the method further comprises administering to the ER⁺ locally advanced or metastatic breast cancer patient an effective amount of cyclin-dependent kinase 4/6 (CDK4/6) inhibitor. In certain embodiments, CDK4/6 inhibitor is palbociclib, abemaciclib, or ribociclib. In some embodiments, the method further comprises administering to the patient an effective amount of mammalian target of rapamycin (mTOR) inhibitor. In certain embodiments, the mTOR inhibitor is Everolimus. In some embodiments, the method further comprises administering to the patient an effective amount of phosphoinositide 3-kinase (PI3K) inhibitor or heat shock protein 90 (HSP90) inhibitor. In some embodiments, the method further comprises administering to the patient an effective amount of human epidermal growth factor receptor 2 (HER2) inhibitor. In certain embodiments, the HER2 inhibitor is trastuzumab (Herceptin®) or ado-trastuzumab emtansine (Kadcyla®). In some embodiments, the method further comprises administering to the patient an effective amount of a histone deacetylase (HDAC) inhibitor. In some of these embodiments, the HDAC inhibitor is vorinostat (Zolinza®), romidepsin (Istodax®), chidamide (Epidaza®), panobinostat (Farydak®), belinostat (Beleodaq®, PXD101), valproic acid (Depakote®, Depakene®, Stavzor®), mocetinostat (MGCD0103), abexinostat (PCI-24781), entinostat (MS-275), pracinostat (SB939), resminostat (4SC-201), givinostat (ITF2357), quisinostat (JNJ-26481585), kevetrin, CUDC-101, AR-42, tefinostat (CHR-2835), CHR-3996, 4SC202, CG200745, rocilinostat (ACY-1215), or sulforaphane. In some embodiments, the method further comprises administering to the patient an effective amount of a checkpoint inhibitor. In some of these embodiments, the checkpoint inhibitor is an antibody specific for programmed cell death protein 1 (PD-1), programmed death-ligand 1 (PD-L1), or cytotoxic T-lymphocyte-associated protein 4 (CTLA-4). In certain embodiments, the PD-1 antibody is pembrolizumab (Keytruda®) or nivolumab (Opdivo®). In certain embodiments, the CTLA-4 antibody is ipilimumab (Yervoy®). In some embodiments, the method further comprises administering to the patient an effective amount of cancer vaccine.

In some embodiments, the patient is premenopausal. In certain embodiments, the patient has locally advanced or metastatic ER+/HER2-breast cancer. In some of these embodiments, the patient has progressed on her first hormonal treatment while on a non-steroid aromatase inhibitor (AI), fulvestrant, AI in combination with a CDK4/6 inhibitor, or fulvestrant in combination with a CDK4/6 inhibitor.

In some embodiments, the patient is perimenopausal. In certain embodiments, the patient has locally advanced or metastatic ER+/HER2− breast cancer. In some of these embodiments, the patient has progressed on her first hormonal treatment while on a non-steroid aromatase inhibitor (AI), fulvestrant, AI in combination with a CDK4/6 inhibitor, or fulvestrant in combination with a CDK4/6 inhibitor.

In some embodiments, the patient is postmenopausal. In certain embodiments, the patient has locally advanced or metastatic ER+/HER2− breast cancer. In some of these embodiments, the patient has progressed on her first hormonal treatment while on a non-steroid aromatase inhibitor (AI), fulvestrant, AI in combination with a CDK4/6 inhibitor, or fulvestrant in combination with a CDK4/6 inhibitor.

In another aspect, a method of treating primary breast cancer in women is presented. The method comprises selecting for treatment a patient who has been diagnosed with estrogen receptor positive (ER⁺) primary breast cancer, and administering to the selected patient an effective amount of a compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant, a pharmaceutically acceptable salt thereof, or a prodrug thereof.

In some embodiments, the compound is administered by oral, intravenous, transdermal, vaginal topical, or vaginal ring administration. In various embodiments, the compound is administered once every day, once every two days, once every three days, once every four days, once every five days, once every six days, once every week, once every two weeks, once every three weeks, or once every month.

In various embodiments, the method of treating ER⁺ primary breast cancer further comprises treating the patient with at least one additional endocrine therapy. In some embodiments, the patient is treated with the additional endocrine therapy at original doses. In some other embodiments, the patient is treated with the additional endocrine therapy at doses higher than original doses. In certain embodiments, the additional endocrine therapy is treatment with lasofoxifene. In certain embodiments the additional endocrine therapy is treatment with an aromatase inhibitor.

In various embodiments, the method further comprises administering to the ER⁺ primary breast cancer patient an effective amount of cyclin-dependent kinase 4/6 (CDK4/6) inhibitor. In certain embodiments, CDK4/6 inhibitor is palbociclib, abemaciclib, or ribociclib. In some embodiments, the method further comprises administering to the patient an effective amount of mammalian target of rapamycin (mTOR) inhibitor. In certain embodiments, the mTOR inhibitor is Everolimus. In some embodiments, the method further comprises administering to the patient an effective amount of phosphoinositide 3-kinase (PI3K) inhibitor or heat shock protein 90 (HSP90) inhibitor. In some embodiments, the method further comprises administering to the patient an effective amount of human epidermal growth factor receptor 2 (HER2) inhibitor. In certain embodiments, the HER2 inhibitor is trastuzumab (Herceptin®) or ado-trastuzumab emtansine (Kadcyla®). In some embodiments, the method further comprises administering to the patient an effective amount of a histone deacetylase (HDAC) inhibitor. In some of these embodiments, the HDAC inhibitor is vorinostat (Zolinza®), romidepsin (Istodax®), chidamide (Epidaza®), panobinostat (Farydak®), belinostat (Beleodaq®, PXD101), valproic acid (Depakote®, Depakene®, Stavzor®), mocetinostat (MGCD0103), abexinostat (PCI-24781), entinostat (MS-275), pracinostat (SB939), resminostat (4SC-201), givinostat (ITF2357), quisinostat (JNJ-26481585), kevetrin, CUDC-101, AR-42, tefinostat (CHR-2835), CHR-3996, 4SC202, CG200745, rocilinostat (ACY-1215), or sulforaphane. In some embodiments, the method further comprises administering to the patient an effective amount of a checkpoint inhibitor. In some of these embodiments, the checkpoint inhibitor is an antibody specific for programmed cell death protein 1 (PD-1), programmed death-ligand 1 (PD-L1), or cytotoxic T-lymphocyte-associated protein 4 (CTLA-4). In certain embodiments, the PD-1 antibody is pembrolizumab (Keytruda®) or nivolumab (Opdivo®). In certain embodiments, the CTLA-4 antibody is ipilimumab (Yervoy®). In some embodiments, the method further comprises administering to the patient an effective amount of cancer vaccine.

In certain embodiments, the patient is premenopausal. In certain embodiments, the patient is perimenopausal. In certain embodiments, the patient is postmenopausal.

In another aspect, a method of adjuvant therapy for estrogen receptor positive (ER+) breast cancer is presented. The method comprises administering to a patient who has received primary treatment for ER+ breast cancer an effective amount of a compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant, a pharmaceutically acceptable salt thereof, or a prodrug thereof, in combination with an aromatase inhibitor.

In some embodiments, the compound is administered continuously during the administration of the aromatase inhibitor. In some embodiments, the compound is administered cyclically during the administration of the aromatase inhibitor. In certain embodiments, the dosing regimen of the compound is different from the dosing regimen of the aromatase inhibitor.

In some embodiments, the aromatase inhibitor is exemestane (Aromasin®), letrozole (Femara®), or anastrozole (Arimidex®). In some embodiments, the compound is administered by oral, intravenous, transdermal, vaginal topical, or vaginal ring administration. In various embodiments, the compound is administered once every day, once every two days, once every three days, once every four days, once every five days, once every six days, once every week, once every two weeks, once every three weeks, or once every month.

In various embodiments, the method of adjuvant therapy for estrogen receptor positive (ER+) breast cancer further comprises treating the patient with at least one additional endocrine therapy. In certain embodiments, the additional endocrine therapy is treatment with lasofoxifene.

In various embodiments, the method of adjuvant therapy for estrogen receptor positive (ER+) breast cancer further comprises administering to the patient an effective amount of cyclin-dependent kinase 4/6 (CDK4/6) inhibitor. In certain embodiments, CDK4/6 inhibitor is palbociclib, abemaciclib, or ribociclib. In some embodiments, the method further comprises administering to the patient an effective amount of mammalian target of rapamycin (mTOR) inhibitor. In certain embodiments, the mTOR inhibitor is Everolimus. In some embodiments, the method further comprises administering to the patient an effective amount of phosphoinositide 3-kinase (PI3K) inhibitor or heat shock protein 90 (HSP90) inhibitor. In some embodiments, the method further comprises administering to the patient an effective amount of human epidermal growth factor receptor 2 (HER2) inhibitor. In certain embodiments, the HER2 inhibitor is trastuzumab (Herceptin®) or ado-trastuzumab emtansine (Kadcyla®). In some embodiments, the method further comprises administering to the patient an effective amount of a histone deacetylase (HDAC) inhibitor. In some of these embodiments, the HDAC inhibitor is vorinostat (Zolinza®), romidepsin (Istodax®), chidamide (Epidaza®), panobinostat (Farydak®), belinostat (Beleodaq®, PXD101), valproic acid (Depakote®, Depakene®, Stavzor®), mocetinostat (MGCD0103), abexinostat (PCI-24781), entinostat (MS-275), pracinostat (SB939), resminostat (4SC-201), givinostat (ITF2357), quisinostat (JNJ-26481585), kevetrin, CUDC-101, AR-42, tefinostat (CHR-2835), CHR-3996, 4SC202, CG200745, rocilinostat (ACY-1215), or sulforaphane. In some embodiments, the method further comprises administering to the patient an effective amount of a checkpoint inhibitor. In some of these embodiments, the checkpoint inhibitor is an antibody specific for programmed cell death protein 1 (PD-1), programmed death-ligand 1 (PD-L1), or cytotoxic T-lymphocyte-associated protein 4 (CTLA-4). In certain embodiments, the PD-1 antibody is pembrolizumab (Keytruda®) or nivolumab (Opdivo®). In certain embodiments, the CTLA-4 antibody is ipilimumab (Yervoy®). In some embodiments, the method further comprises administering to the patient an effective amount of cancer vaccine.

In certain embodiments, the patient is premenopausal. In certain embodiments, the patient is perimenopausal. In certain embodiments, the patient is postmenopausal.

In another aspect, a method of treating cancers other than breast cancer in women is presented. The method comprises selecting for treatment a patient who has been diagnosed with estrogen receptor positive (ER⁺) cancer, other than breast cancer, and has at least one gain of function mutations in the Estrogen Receptor 1 (ESR1) gene, and administering to the selected patient an effective amount of a compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant, a pharmaceutically acceptable salt thereof, or a prodrug thereof. In some embodiments, the patient has been diagnosed with ER⁺ ovarian cancer. In some other embodiments, the patient has been diagnosed with ER⁺ lung cancer.

In some embodiments, the compound is administered by oral, intravenous, transdermal, vaginal topical, or vaginal ring administration. In various embodiments, the compound is administered once every day, once every two days, once every three days, once every four days, once every five days, once every six days, once every week, once every two weeks, once every three weeks, or once every month.

In various embodiments, the method of treating ER⁺ cancer, other than breast cancer, further comprises treating the patient with at least one additional endocrine therapy. In some embodiments, the patient is treated with the additional endocrine therapy at original doses. In some other embodiments, the patient is treated with the additional endocrine therapy at doses higher than original doses. In certain embodiments, the additional endocrine therapy is treatment with lasofoxifene. In certain embodiments the additional endocrine therapy is treatment with an aromatase inhibitor.

In various embodiments, the method further comprises administering to the patient with ER⁺ cancer, other than breast cancer, an effective amount of cyclin-dependent kinase 4/6 (CDK4/6) inhibitor. In certain embodiments, CDK4/6 inhibitor is palbociclib, abemaciclib, or ribociclib. In some embodiments, the method further comprises administering to the patient an effective amount of mammalian target of rapamycin (mTOR) inhibitor. In certain embodiments, the mTOR inhibitor is Everolimus. In some embodiments, the method further comprises administering to the patient an effective amount of phosphoinositide 3-kinase (PI3K) inhibitor or heat shock protein 90 (HSP90) inhibitor. In some embodiments, the method further comprises administering to the patient an effective amount of human epidermal growth factor receptor 2 (HER2) inhibitor. In certain embodiments, the HER2 inhibitor is trastuzumab (Herceptin®) or ado-trastuzumab emtansine (Kadcyla®). In some embodiments, the method further comprises administering to the patient an effective amount of a histone deacetylase (HDAC) inhibitor. In some of these embodiments, the HDAC inhibitor is vorinostat (Zolinza®), romidepsin (Istodax®), chidamide (Epidaza®), panobinostat (Farydak®), belinostat (Beleodaq®, PXD101), valproic acid (Depakote®, Depakene®, Stavzor®), mocetinostat (MGCD0103), abexinostat (PCI-24781), entinostat (MS-275), pracinostat (SB939), resminostat (4SC-201), givinostat (ITF2357), quisinostat (JNJ-26481585), kevetrin, CUDC-101, AR-42, tefinostat (CHR-2835), CHR-3996, 4SC202, CG200745, rocilinostat (ACY-1215), or sulforaphane. In some embodiments, the method further comprises administering to the patient an effective amount of a checkpoint inhibitor. In some of these embodiments, the checkpoint inhibitor is an antibody specific for programmed cell death protein 1 (PD-1), programmed death-ligand 1 (PD-L1), or cytotoxic T-lymphocyte-associated protein 4 (CTLA-4). In certain embodiments, the PD-1 antibody is pembrolizumab (Keytruda®) or nivolumab (Opdivo®). In certain embodiments, the CTLA-4 antibody is ipilimumab (Yervoy®). In some embodiments, the method further comprises administering to the patient an effective amount of cancer vaccine.

In certain embodiments, the patient is premenopausal. In certain embodiments, the patient is perimenopausal. In certain embodiments, the patient is postmenopausal.

In another aspect, a method of treating a female patient suffering from breast cancer who is at risk of acquiring a gain of function missense mutation within the ligand binding domain (LBD) of the Estrogen Receptor 1 (ESR1) gene is presented. The method comprises administering to the female patient an effective amount of a compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant, a pharmaceutically acceptable salt thereof, or a prodrug thereof.

In another aspect, a method of treating a female patient suffering from breast cancer who is at risk of acquiring resistance to endocrine therapy is presented. The endocrine therapy is optionally (i) selective ER modulator (SERM) therapy, (ii) selective ER degrader (SERD) therapy, (iii) aromatase inhibitor (AI) therapy, or (iv) any combination of (i), (ii) and/or (iii). The method comprises administering to the female patient an effective amount of a compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant, a pharmaceutically acceptable salt thereof, or a prodrug thereof.

In some embodiments, the patient has primary breast cancer. In some of these embodiments, the primary breast cancer is locally advanced.

In various embodiments, the patient has been treated with endocrine therapy, optionally wherein the endocrine therapy is (i) selective ER modulator (SERM) therapy, (ii) selective ER degrader (SERD) therapy, (iii) aromatase inhibitor (AI) therapy, or (iv) any combination of (i), (ii) and/or (iii).

In another aspect, a method of treating a female patient suffering from estrogen receptor positive (ER+) primary breast cancer is presented. The method comprises administering to a female patient an effective amount of a compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant, a pharmaceutically acceptable salt thereof, or a prodrug thereof.

In some embodiments, the patient is at risk of acquiring resistance to endocrine therapy, optionally wherein the endocrine therapy is (i) selective ER modulator (SERM) therapy, (ii) selective ER degrader (SERD) therapy, (iii) aromatase inhibitor (AI) therapy, or (iv) any combination of (i), (ii) and/or (iii).

In certain embodiments, the primary breast cancer is locally advanced.

In some embodiments, the patient has been treated with endocrine therapy, optionally wherein the endocrine therapy is (i) selective ER modulator (SERM) therapy, (ii) selective ER degrader (SERD) therapy, (iii) aromatase inhibitor (AI) therapy, or (iv) any combination of (i), (ii) and/or (iii).

In another aspect, a method of treating a female patient suffering from estrogen receptor positive (ER+) locally advanced or metastatic breast cancer is presented. The method comprises administering to a female patient an effective amount of a compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant, a pharmaceutically acceptable salt thereof, or a prodrug thereof.

In various embodiments, the selected patient has previously been treated with one or more lines of endocrine therapy. In certain embodiments, the patient has previously been treated with a plurality of lines of endocrine therapy.

In some embodiments, the endocrine therapy that the patient has previously been treated with is a selective ER modulator (SERM). In some embodiments, the endocrine therapy that the patient has previously been treated with is a selective ER degrader (SERD).

In some embodiments, the endocrine therapy that the patient has previously been treated with is an aromatase inhibitor. In certain embodiments, the aromatase inhibitor is exemestane (Aromasin®), letrozole (Ferrara®), or anastrozole (Arimidex®).

In various embodiments, the patient's cancer has at least one gain of function missense mutation within the ligand binding domain (LBD) of the Estrogen Receptor 1 (ESR1) gene. In some embodiments, the patient has previously been determined to have at least one gain of function missense mutation within the ligand binding domain (LBD) of the Estrogen Receptor 1 (ESR1) gene. In certain embodiments, the method further comprises determining that the patient has at least one gain of function missense mutation within the ligand binding domain (LBD) of the Estrogen Receptor 1 (ESR1) gene.

In some embodiments, the at least one of gain of function missense mutation is in any one of amino acids D538, Y537, L536, P535, V534, S463, V392, or E380.

In certain embodiments, the at least one gain of function missense mutation is in the amino acid D538. In some preferred embodiments the mutation is D538G.

In certain embodiments, the at least one gain of function missense mutation is in the amino acid Y537. In some embodiments, the mutation is Y537S, Y537N, Y537C, or Y537Q. In some preferred embodiments, the mutation is Y537C.

In certain embodiments, the at least one gain of function missense mutation is in the amino acid L536. In some embodiments, the mutation is L536R or L536Q.

In certain embodiments, the at least one gain of function missense mutation is in the amino acid P535. In some embodiments, the mutation is P535H.

In certain embodiments, the at least one gain of function missense mutation is in the amino acid V534. In some embodiments, the mutation is V534E.

In certain embodiments, the at least one gain of function missense mutation is in the amino acid S463. In some embodiments, the mutation is S463P.

In certain embodiments, the at least one gain of function missense mutation is in the amino acid V392. In some embodiments, the mutation is V392I.

In certain embodiments, the at least one gain of function missense mutation is in the amino acid E380. In some embodiments, the mutation is E380Q.

In various embodiments, the compound is administered by oral, intravenous, transdermal, vaginal topical, or vaginal ring administration. In various embodiments, the compound is administered once every day, once every two days, once every three days, once every four days, once every five days, once every six days, once every week, once every two weeks, once every three weeks, or once every month.

In certain embodiments, the method further comprises treating the patient with at least one additional endocrine therapy. In some embodiments, the patient is treated with the additional endocrine therapy at original doses. In some other embodiments, the patient is treated with the additional endocrine therapy at doses higher than original doses. In certain embodiments, the additional endocrine therapy is treatment with lasofoxifene. In certain embodiments, the additional endocrine therapy is treatment with an aromatase inhibitor.

In various embodiments, the method further comprises administering to the ER⁺ locally advanced or metastatic breast cancer patient an effective amount of cyclin-dependent kinase 4/6 (CDK4/6) inhibitor. In certain embodiments, CDK4/6 inhibitor is palbociclib, abemaciclib, or ribociclib. In some embodiments, the method further comprises administering to the patient an effective amount of mammalian target of rapamycin (mTOR) inhibitor. In certain embodiments, the mTOR inhibitor is Everolimus. In some embodiments, the method further comprises administering to the patient an effective amount of phosphoinositide 3-kinase (PI3K) inhibitor or heat shock protein 90 (HSP90) inhibitor. In some embodiments, the method further comprises administering to the patient an effective amount of human epidermal growth factor receptor 2 (HER2) inhibitor. In certain embodiments, the HER2 inhibitor is trastuzumab (Herceptin®) or ado-trastuzumab emtansine (Kadcyla®). In some embodiments, the method further comprises administering to the patient an effective amount of a histone deacetylase (HDAC) inhibitor. In some of these embodiments, the HDAC inhibitor is vorinostat (Zolinza®), romidepsin (Istodax®), chidamide (Epidaza®), panobinostat (Farydak®), belinostat (Beleodaq®, PXD101), valproic acid (Depakote®, Depakene®, Stavzor®), mocetinostat (MGCD0103), abexinostat (PCI-24781), entinostat (MS-275), pracinostat (SB939), resminostat (4SC-201), givinostat (ITF2357), quisinostat (JNJ-26481585), kevetrin, CUDC-101, AR-42, tefinostat (CHR-2835), CHR-3996, 4SC202, CG200745, rocilinostat (ACY-1215), or sulforaphane. In some embodiments, the method further comprises administering to the patient an effective amount of a checkpoint inhibitor. In some of these embodiments, the checkpoint inhibitor is an antibody specific for programmed cell death protein 1 (PD-1), programmed death-ligand 1 (PD-L1), or cytotoxic T-lymphocyte-associated protein 4 (CTLA-4). In certain embodiments, the PD-1 antibody is pembrolizumab (Keytruda®) or nivolumab (Opdivo®). In certain embodiments, the CTLA-4 antibody is ipilimumab (Yervoy®). In some embodiments, the method further comprises administering to the patient an effective amount of cancer vaccine.

In some embodiments, the patient is premenopausal. In certain embodiments, the patient has locally advanced or metastatic ER+/HER2− breast cancer. In some of these embodiments, the patient has progressed on her first hormonal treatment while on a non-steroid aromatase inhibitor (AI), fulvestrant, AI in combination with a CDK4/6 inhibitor, or fulvestrant in combination with a CDK4/6 inhibitor.

In some embodiments, the patient is perimenopausal. In certain embodiments, the patient has locally advanced or metastatic ER+/HER2− breast cancer. In some of these embodiments, the patient has progressed on her first hormonal treatment while on a non-steroid aromatase inhibitor (AI), fulvestrant, AI in combination with a CDK4/6 inhibitor, or fulvestrant in combination with a CDK4/6 inhibitor.

In some embodiments, the patient is postmenopausal. In certain embodiments, the patient has locally advanced or metastatic ER+/HER2− breast cancer. In some of these embodiments, the patient has progressed on her first hormonal treatment while on a non-steroid aromatase inhibitor (AI), fulvestrant, AI in combination with a CDK4/6 inhibitor, or fulvestrant in combination with a CDK4/6 inhibitor.

5. BRIEF DESCRIPTION OF THE DRAWINGS

These and other features, aspects, and advantages of the present invention will become better understood with regard to the following description, and accompanying drawings, where:

FIGS. 1A, 1B, 1C, 1D, 1E, and 1F show the effects of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant on ESR1 wild type and ligand binding domain (“LBD”) mutations in Caov2 ovarian carcinoma cells, with FIG. 1A demonstrating that the mutant receptors are constitutively active and do not respond to 17-β estradiol (“E2”), FIG. 1B demonstrating that raloxifene, bazedoxifene, 4-hydroxytamoxifen (“4OHT”), the 4-hydroxy metabolite of etacstil (“GW-7604”), and fulvestrant (“ICI”) each inhibits activity of the ESR1 wild type receptor, FIG. 1C showing that raloxifene, bazedoxifene, 4-hydroxytamoxifen (4OHT), the 4-hydroxy metabolite of etacstil (GW-7604), and fulvestrant (ICI) each inhibits the Y537N mutant receptor activity in a dose-response manner, FIG. 1D demonstrating that raloxifene, bazedoxifene, 4-hydroxytamoxifen (4OHT), the 4-hydroxy metabolite of etacstil (GW-7604), and fulvestrant (ICI) each inhibits the Y537S mutant receptor activity in a dose-response manner, FIG. 1E demonstrating that raloxifene, bazedoxifene, 4-hydroxytamoxifen (4OHT), the 4-hydroxy metabolite of etacstil (GW-7604), and fulvestrant (ICI) each inhibits the Y537C mutant receptor activity in a dose-response manner, and FIG. 1F demonstrating that raloxifene, bazedoxifene, 4-hydroxytamoxifen (4OHT), the 4-hydroxy metabolite of etacstil (GW-7604), and fulvestrant (ICI) each inhibits the D538G mutant receptor activity in a dose-response manner.

FIGS. 2A, 2B, 2C, 2D, and 2E show the effects of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant on ESR1 wild type and LBD mutations in Caov2 ovarian carcinoma cells, with FIG. 2A demonstrating that fulvestrant (ICI) inhibits the ESR1 wild type and the ESR1 LBD mutant receptor activity, FIG. 2B demonstrating that 4-hydroxytamoxifen (4OHT) inhibits the ESR1 wild type and the ESR1 LBD mutant receptor activity, FIG. 2C demonstrating that raloxifene inhibits the ESR1 wild type and the ESR1 LBD mutant receptor activity, FIG. 2D demonstrating that bazedoxifene inhibits the ESR1 wild type and the ESR1 LBD mutant receptor activity, and FIG. 2E demonstrating that the 4-hydroxy metabolite of etacstil (GW-7604) inhibits the ESR1 wild type and the ESR1 LBD mutant receptor activity.

FIGS. 3A, 3B, 3C, 3D, 3E, and 3F show the effects of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant on ESR1 wild type and LBD mutations in SKBR3 breast adenocarcinoma cells, with FIG. 3A demonstrating that the mutant receptors are constitutively active and do not respond to 17-β estradiol (E2), FIG. 3B demonstrating that raloxifene, bazedoxifene, 4-hydroxytamoxifen (4OHT), the 4-hydroxy metabolite of etacstil (GW-7604), and fulvestrant (ICI) each inhibits the ESR1 wild type receptor activity, FIG. 3C demonstrating that raloxifene, bazedoxifene, 4-hydroxytamoxifen (4OHT), the 4-hydroxy metabolite of etacstil (GW-7604), and fulvestrant (ICI) each inhibits the Y537N mutant receptor activity in a dose-response manner, FIG. 3D showing that raloxifene, bazedoxifene, 4-hydroxytamoxifen (4OHT), the 4-hydroxy metabolite of etacstil (GW-7604), and fulvestrant (ICI) each inhibits the Y537S mutant receptor activity in a dose-response manner, FIG. 3E demonstrating that raloxifene, bazedoxifene, 4-hydroxytamoxifen (4OHT), the 4-hydroxy metabolite of etacstil (GW-7604), and fulvestrant (ICI) each inhibits the Y537C mutant receptor activity in a dose-response manner, and FIG. 3F demonstrating that raloxifene, bazedoxifene, 4-hydroxytamoxifen (4OHT), the 4-hydroxy metabolite of etacstil (GW-7604), and fulvestrant (ICI) each inhibits the D538G mutant receptor activity in a dose-response manner.

FIGS. 4A, 4B, 4C, 4D, and 4E show the effects of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant on ESR1 wild type and LBD mutations in SKBR3 breast adenocarcinoma cells, with FIG. 4A demonstrating that fulvestrant (ICI) inhibits the ESR1 wild type and the ESR1 LBD mutant receptor activity, FIG. 4B showing that 4-hydroxytamoxifen (4OHT) inhibits the ESR1 wild type and the ESR1 LBD mutant receptor activity, FIG. 4C demonstrating that raloxifene inhibits the ESR1 wild type and the ESR1 LBD mutant receptor activity, FIG. 4D demonstrating that bazedoxifene inhibits the ESR1 wild type and the ESR1 LBD mutant receptor activity, and FIG. 4E demonstrating that the 4-hydroxy metabolite of etacstil (GW-7604) inhibits the ESR1 wild type and the ESR1 LBD mutant receptor activity.

6. DETAILED DESCRIPTION OF THE INVENTION

Endocrine therapy is often used for treatment and prevention of ER⁺ breast cancers. Different types of endocrine therapy include selective ER modulators (SERMs), selective ER degraders (SERDs), and aromatase inhibitors (AIs). Although endocrine therapy has led to a significant improvement in outcome for women with ER⁺ breast cancer, its effectiveness is limited by intrinsic and acquired endocrine resistance. Recent studies on the mechanism of endocrine resistance have demonstrated that in some cases Estrogen Receptor 1 (ESR1) gene mutations lead to the conformational change of the ERα protein towards a constitutively active state and result in ligand-independent activity. See Jeselsohn et al., Clinical Cancer Research 20(7): 1757-1767 (2014).

Using cell lines with engineered mutations in the ESR1 gene, we discovered that raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant each inhibits the mutant receptor activity in a dose-responsive manner, newly making possible methods of treating ER⁺ locally advanced or metastatic breast cancer, ER⁺ primary breast cancer, and other ER⁺ cancers, including cancers having ESR1 mutations, using raloxifene, bazedoxifene, tamoxifen, etacstil, or fulvestrant, whose effectiveness is not precluded by endocrine resistance.

6.1. Methods of Treatment

Accordingly, in a first aspect, disclosed herein are methods of treating cancers in women, comprising selecting for treatment a patient who has been diagnosed with estrogen receptor positive (ER⁺) cancer. The selected patient is treated with an effective amount of a compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant, a pharmaceutically acceptable salt thereof, or a prodrug thereof.

6.1.1. Patient with ER⁺ Cancer

In various embodiments, the patient has been diagnosed with ER⁺ cancer by immunohistochemistry (IHC) performed on a sample of the patient's cancer.

In some embodiments, the patient has been diagnosed with locally advanced or metastatic ER⁺ breast cancer. In some embodiments, the patient has been diagnosed with ER⁺ primary breast cancer. In some embodiments, the patient has been diagnosed with an ER⁺ cancer other than breast cancer. In some of these embodiments, the patient has been diagnosed with ER⁺ ovarian cancer. In some of these embodiments, the patient has been diagnosed with ER⁺ lung cancer.

In some embodiments, cells of the patient's cancer have acquired a gain of function missense mutation within the ligand binding domain (LBD) of the Estrogen Receptor 1 (ESR1) gene.

In some embodiments, the patient is at risk of acquiring resistance to endocrine therapy. In particular embodiments, the patient is at risk of acquiring resistance to endocrine therapy due to the increased expression of estrogen receptor. In particular embodiments, the patient is at risk of acquiring resistance to endocrine therapy due to the increased expression of co-activators of estrogen receptor. In particular embodiments, the patient is at risk of acquiring resistance to endocrine therapy due to increased phosphorylation level and activity of estrogen receptor and its co-activators. In particular embodiments, the patient is at risk of acquiring resistance to endocrine therapy due to change of tumor microenvironment and other host related factors. In some preferred embodiments, the patient is at risk of acquiring resistance to endocrine therapy due to mutations in the Estrogen Receptor 1 (ESR1) gene.

In various embodiments, resistance to endocrine therapy is resistance to (i) selective ER modulator (SERM) therapy, (ii) selective ER degrader (SERD) therapy, (iii) aromatase inhibitor (AI) therapy, or (iv) any combination of (i), (ii) and/or (iii).

6.1.2. Previous Treatment with Endocrine Therapy

In various embodiments, the ER⁺ cancer patient has previously been treated with one or more lines of endocrine therapy. In certain embodiments, the patient has previously been treated with one line of endocrine therapy. In certain other embodiments, the patient has previously been treated with a plurality of lines of endocrine therapy. In some embodiments, the patient has previously been treated with two lines of endocrine therapy. In some embodiments, the patient has previously been treated with three lines of endocrine therapy. In some embodiments, the patient has previously been treated with four or more lines of endocrine therapy.

In some embodiments, the endocrine therapy that the patient has previously been treated with is a selective ER modulator (SERM).

In some embodiments, the endocrine therapy that the patient has previously been treated with is a selective ER degrader (SERD). In various embodiments, the selective ER degrader binds to the estrogen receptor and leads to the proteasomal degradation of the receptor.

In some embodiments, the endocrine therapy with which the patient has previously been treated is an aromatase inhibitor (AI). In various embodiments, the aromatase inhibitor blocks the production of estrogen. In some embodiments, the aromatase inhibitor is selected from exemestane (Aromasin®), letrozole (Ferrara®), and anastrozole (Arimidex®).

In some embodiments, the endocrine therapy that the patient has previously been treated with is ovarian suppression. In certain embodiments, ovarian suppression is achieved by oophorectomy. In certain embodiments, ovarian suppression is achieved by administration of a GnRH antagonist.

In certain embodiments, the patient's cancer has progressed or relapsed after the previous endocrine therapy treatment. In some embodiments, the patient's cancer has progressed or relapsed after aromatase inhibitor treatment. In some of these embodiments, the patient's cancer has progressed or relapsed after multiple lines of endocrine therapy treatment.

In some embodiments, the ER⁺ cancer patient has not been treated previously with endocrine therapy.

In certain embodiments, the patient is resistant to endocrine therapy. In some embodiments, the patient has intrinsic endocrine resistance. In some embodiments, the patient has acquired endocrine resistance. In particular embodiments, the patient is resistant to endocrine therapy due to the increased expression of estrogen receptor. In particular embodiments, the patient is resistant to endocrine therapy due to the increased expression of co-activators of estrogen receptor. In particular embodiments, the patient is resistant to endocrine therapy due to increased phosphorylation level and activity of estrogen receptor and its co-activators. In particular embodiments, the patient is resistant to endocrine therapy due to change of tumor microenvironment and other host related factors. In some preferred embodiments, the patient is resistant to endocrine therapy due to gene mutations in the Estrogen Receptor 1 (ESR1) gene.

In various embodiments, the patient is resistant to clinical doses of one or more SERMs. In various embodiments, the patient is resistant to clinical doses of one or more SERDs. In various embodiments, the patient is resistant to clinical doses of one or more aromatase inhibitors. In various embodiments, the patient is resistant to higher than clinical doses of one or more SERMs. In various embodiments, the patient is resistant to higher than clinical doses of one or more SERDs. In various embodiments, the patient is resistant to higher than clinical doses of one or more aromatase inhibitors.

In certain embodiments, the ER⁺ cancer patient has not been demonstrated to have endocrine resistance. In some of these embodiments, the patient has not been demonstrated to have endocrine resistance due to the limitations of the detection methods.

In some embodiments, the compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant is administered to the ER⁺ cancer patient after completion of cancer treatment. In some of these embodiments, the compound is administered to the patient to treat occult micrometastasis.

6.1.3. Menopause Status

In some embodiments, the ER⁺ cancer patient is premenopausal. In specific embodiments, the patient is premenopausal and has locally advanced or metastatic ER⁺ cancer. In particular embodiments, the patient is premenopausal and has locally advanced or metastatic ER⁺ breast cancer.

In certain embodiments, the ER⁺ cancer patient is perimenopausal. In specific embodiments, the patient is perimenopausal and has locally advanced or metastatic ER⁺ cancer. In particular embodiments, the patient is perimenopausal and has locally advanced or metastatic ER⁺ breast cancer.

In typical embodiments, the ER⁺ cancer patient is postmenopausal. In specific embodiments, the patient is postmenopausal and has locally advanced or metastatic ER⁺ cancer. In particular embodiments, the patient is postmenopausal and has locally advanced or metastatic ER⁺ breast cancer.

In certain embodiments, the compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant is administered to a premenopausal woman with locally advanced or metastatic ER⁺/HER2⁻ breast cancer. In certain embodiments, the compound is administered to a premenopausal woman with locally advanced or metastatic ER⁺/HER2⁻ breast cancer who has progressed while on her first hormonal treatment with a non-steroid aromatase inhibitor (AI), fulvestrant, AI in combination with a CDK4/6 inhibitor, or fulvestrant in combination with a CDK4/6 inhibitor.

In certain embodiments, the compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant is administered to a perimenopausal woman with locally advanced or metastatic ER⁺/HER2⁻ breast cancer. In certain embodiments, the compound is administered to a perimenopausal woman with locally advanced or metastatic ER⁺/HER2⁻ breast cancer who has progressed while on her first hormonal treatment with a non-steroid aromatase inhibitor (AI), fulvestrant, AI in combination with a CDK4/6 inhibitor, or fulvestrant in combination with a CDK4/6 inhibitor.

In certain embodiments, the compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant is administered to a postmenopausal woman with locally advanced or metastatic ER⁺/HER2⁻ breast cancer. In certain embodiments, the compound is administered to a postmenopausal woman with locally advanced or metastatic ER⁺/HER2⁻ breast cancer who has progressed while on her first hormonal treatment with a non-steroid aromatase inhibitor (AI), fulvestrant, AI in combination with a CDK4/6 inhibitor, or fulvestrant in combination with a CDK4/6 inhibitor.

6.1.4. Mutations in ESR1 Gene

In various embodiments, the patient has an ER⁺ cancer, cells of which have at least one mutation in the Estrogen Receptor 1(ESR1) gene, which encodes the Estrogen Receptor α (ERα) protein. In some embodiments, the mutation leads to the ligand-independent activity of the estrogen receptor. In some embodiments, the mutation leads to enhanced ligand stimulated activity of estrogen receptor. In some embodiments, the mutation leads to resistance to endocrine therapy. In some embodiments, the mutation promotes tumor growth. In some embodiments, the mutation enhances metastatic activity of cancer. In some preferred embodiments, the mutation enhances metastatic activity of ER⁺ metastatic breast cancer.

In some embodiments, the mutation arises from a rare and undetectable pre-existing clone. In some embodiments, the mutation is acquired de novo during the course of endocrine therapy treatment. In some preferred embodiments, the mutation is acquired de novo during the course of endocrine therapy treatment of breast cancer. In some embodiments, the mutation is acquired de novo after multiple lines of endocrine therapy treatment. In some embodiments, the mutation is acquired de novo after multiple lines of endocrine therapy treatment of metastatic breast cancer. In various embodiments, the mutant clone expands to become a more dominant clone over the course of successive lines of endocrine therapy.

In some embodiments, the mutation in the ESR1 gene is missense point mutation. In some embodiments, the mutation in the ESR1 gene is truncating mutation. In some embodiments, the mutation in the ESR1 gene is gene amplification. In some embodiments, the mutation in the ESR1 gene is genomic rearrangement.

In some preferred embodiments, the patient has an ER⁺ cancer that has at least one gain of function missense mutation within the ligand binding domain (LBD) of the ESR1 gene. In various embodiments, at least one of the mutations is in an amino acid selected from D538, Y537, L536, P535, V534, S463, V392, and E380. (The amino acids are numbered according to the ESR1 protein with the NCBI accession number NP_000116.2.)

In particular embodiments, the mutation increases the stability of the agonist conformation of Helix 12 of the ERα protein. In some of these embodiments, the mutation increases the binding of the estrogen receptor to its co-activators. In some of these embodiments, the mutation leads to hormone independent activity of estrogen receptor. In some of these embodiments, the mutation leads to resistance to a SERM, a SERD, and/or an aromatase inhibitor.

In certain embodiments, the mutation is in the amino acid D538. In certain preferred embodiments, the mutation is D538G.

In certain embodiments, the mutation is in the amino acid Y537. In some of these embodiments, the mutation is Y537S, Y537N, Y537C, or Y537Q. In certain preferred embodiments, the mutation is Y537C.

In some embodiments, the mutation is in the amino acid L536. In certain embodiments, the mutation is L536R or L536Q.

In some embodiments, the mutation is in the amino acid P535. In certain embodiments, the mutation is P535H.

In some embodiments, the mutation is in the amino acid V534. In certain embodiments, the mutation is V534E.

In some embodiments, the mutation is in the amino acid S463. In certain embodiments, the mutation is S463P.

In some embodiments, the mutation is in the amino acid V392. In certain embodiments, the mutation is V392I.

In some embodiments, the mutation is in the amino acid E380. In certain embodiments, the mutation is E380Q.

6.1.4.1. Detection of the ESR1 Gene Mutations

In various embodiments, the patient has been previously determined to have at least one mutation in the ESR1 gene. Some embodiments of the methods described herein further include the step of detecting mutations in the ESR1 gene.

In some embodiments, massively parallel next generation sequencing (NGS) is used for detecting the estrogen receptor mutations in the patient's cancer. In certain embodiments, the entire genome is sequenced. In certain embodiments, selected gene panels of cancer-related genes are sequenced. In certain embodiments, all coding exons within a given set of genes are sequenced. In certain embodiments, known “hotspot” regions within a given set of genes are sequenced. However, the inherent error rate of current next generation sequencing techniques is up to 1%, limiting the sensitivity and specificity of detection. In some embodiments, targeted sequencing is used for detecting the presence of the ESR1 mutations. Although targeted sequencing allows deeper sequencing, it is also currently limited by the 1% error rate. In some embodiments, methods with reduced sequencing error rate are used. In a particular embodiment, Safe-Sequencing System (Safe-SeqS) is used, which tags each template molecule to allow for confident identification of rare variants. See Kinde et al., Proceedings of the National Academy of Sciences 108(23): 9530-9535 (2011). In particular embodiments, ultrasensitive Duplex sequencing is used, which independently tags and sequences each of the two strands of a DNA duplex. See Schmitt et al., Proceedings of the National Academy of Sciences 109(36): 14508-14513 (2012). In some embodiments, digital droplet PCR is used, which emulsifies DNA in thousands to millions of droplets to encapsulate single DNA molecules, designed with mutant specific primers. See Vogelstein and Kinzler, Proceedings of the National Academy of Sciences 96(16): 2322-2326 (1999) and Huggett et al., Clinical Chemistry 61(1): 79-88 (2014).

In some embodiments, the detection of the ESR1 mutations takes place at the initial diagnosis. In some embodiments, the detection of the mutations takes place at the time of disease progression, relapse, or recurrence. In some embodiments, the detection of the mutations takes place at the time of disease progression. In some embodiments, the detection of the mutations takes place at the time when the disease is stable.

In some embodiments, one or more tissue specimens are obtained for detection of the mutations. In certain embodiments, the tissue specimen is a tumor biopsy. In certain embodiments, the tissue specimen is a biopsy of metastases. In some other embodiments, liquid biopsies are obtained for detection of the mutations. In certain embodiments, the liquid biopsy is circulating tumor cells (CTCs). In certain other embodiments, the liquid biopsy is cell-free DNA from blood samples.

In specific embodiments, the ESR1 mutations are monitored by circulating tumor DNA (ctDNA) analysis. In some embodiments, the ctDNA analysis is performed throughout the course of treatment. In some of these embodiments, the ctDNA is extracted from patient blood samples. In certain embodiments, the ctDNA is evaluated by digital PCR analysis of the ESR1 mutations.

6.1.5. Estradiol Levels

In various embodiments, the patient selected for treatment based on presence of ESR1 gene mutations is further selected based on serum estradiol level.

In certain embodiments, the serum estradiol level of the patient with the ER⁺ cancer having an ESR1 gene mutation is at least 0.20 ng/dL, such as at least 0.25 ng/dL, at least 0.30 ng/dL, at least 0.35 ng/dL, at least 0.40 ng/dL, at least 0.45 ng/dL, at least 0.50 ng/dL, at least 0.55 ng/dL, at least 0.60 ng/dL, at least 0.65 ng/dL, at least 0.70 ng/dL, at least 0.75 ng/dL, at least 0.80 ng/dL, at least 0.85 ng/dL, at least 0.90 ng/dL, at least 0.95 ng/dL, or at least 1.0 ng/dL.

In certain embodiments, the serum estradiol level of the patient with the ESR1 gene mutation is about 0.20 ng/dL to about 1.0 ng/dL, such as about 0.20 ng/dL to about 0.25 ng/dL, about 0.25 ng/dL to about 0.30 ng/dL, about 0.30 ng/dL to about 0.35 ng/dL, about 0.35 ng/dL to about 0.40 ng/dL, about 0.40 ng/dL to about 0.45 ng/dL, about 0.45 ng/dL to about 0.50 ng/dL, about 0.50 ng/dL to about 0.55 ng/dL, about 0.55 ng/dL to about 0.60 ng/dL, about 0.60 ng/dL to about 0.65 ng/dL, about 0.65 ng/dL to about 0.70 ng/dL, about 0.70 ng/dL to about 0.75 ng/dL, about 0.75 ng/dL to about 0.80 ng/dL, about 0.80 ng/dL to about 0.85 ng/dL, about 0.85 ng/dL to about 0.90 ng/dL, about 0.90 ng/dL to about 0.95 ng/dL, about 0.95 ng/dL to about 1.0 ng/dL.

6.1.6. Adjuvant Treatment

In various embodiments, the compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant is administered to the patient as adjuvant treatment. In certain embodiments, the compound is administered to the patient as adjuvant treatment alone. In certain other embodiments, the compound is administered to the patient as adjuvant treatment in combination with other endocrine therapies. In some embodiments, the compound is administered to the patient after the primary treatment. In some of these embodiments, the compound is administered to the patient after surgical removal or debulking of the cancer.

In some embodiments, the compound is administered to the patient as adjuvant therapy in combination with an aromatase inhibitor (AI). In various embodiments, the aromatase inhibitor is exemestane (Aromasin®), letrozole (Ferrara®), or anastrozole (Arimidex®).

In some embodiments, the compound is administered continuously during the administration of the aromatase inhibitor. In some other embodiments, the compound is administered cyclically during the administration of the aromatase inhibitor. In some embodiments, the compound and the aromatase inhibitor are administered together (simultaneously). In some other embodiments, the compound and the aromatase inhibitor are administered separately (sequentially).

In certain embodiments, the dosing regimen of the compound is different from the dosing regimen of the aromatase inhibitor. In some of these embodiments, the dosing quantity of the compound is different from the dosing quantity of the aromatase inhibitor. In some embodiments, the dosing schedule of the compound is different from the dosing schedule of the aromatase inhibitor. In some embodiments, the route of administration of the compound is different from the route of administration of the aromatase inhibitor.

In certain embodiments, the dosing regimen of the compound is the same as the dosing regimen of the aromatase inhibitor. In some embodiments, the dosing quantity of the compound is the same as the dosing quantity of the aromatase inhibitor. In some embodiments, the dosing schedule of the compound is the same as the dosing schedule of the aromatase inhibitor. In some embodiments, the route of administration of the compound is the same as the route of administration of the aromatase inhibitor.

In some embodiments, the compound is administered as adjuvant therapy in combination with an aromatase inhibitor to the patient for one year. In some embodiments, the compound is administered as adjuvant therapy in combination with an aromatase inhibitor to the patient for two years. In some embodiments, the compound is administered as adjuvant therapy in combination with an aromatase inhibitor to the patient for three years. In some embodiments, the compound is administered as adjuvant therapy in combination with an aromatase inhibitor to the patient for four years. In some embodiments, the compound is administered as adjuvant therapy in combination with an aromatase inhibitor to the patient for five years. In some embodiments, the compound is administered as adjuvant therapy in combination with an aromatase inhibitor to the patient for six years. In some embodiments, the compound is administered as adjuvant therapy in combination with an aromatase inhibitor to the patient for seven years. In some embodiments, the compound is administered as adjuvant therapy in combination with an aromatase inhibitor to the patient for eight years. In some embodiments, the compound is administered as adjuvant therapy in combination with an aromatase inhibitor to the patient for nine years. In some embodiments, the compound is administered as adjuvant therapy in combination with an aromatase inhibitor to the patient for ten years. In some other embodiments, the compound is administered as adjuvant therapy in combination with an aromatase inhibitor to the patient for more than ten years. In certain embodiments, the compound is administered as adjuvant therapy in combination with an aromatase inhibitor until the patient's cancer progresses on therapy.

In some embodiments, the compound is administered as adjuvant therapy in combination with an aromatase inhibitor to increase the disease-free survival of the breast cancer patient. In some embodiments, the compound is administered as adjuvant therapy in combination with an aromatase inhibitor to decrease the incidence of contralateral breast cancer. In some embodiments, the compound is administered as adjuvant therapy in combination with an aromatase inhibitor to prevent the recurrence and progression of the cancer.

6.2. Raloxifene, Bazedoxifene, Tamoxifen, Etacstil, and Fulvestrant

In various embodiments, the selected patient is treated with an effective amount of a compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant, a pharmaceutically acceptable salt thereof, or a prodrug thereof. In certain embodiments, the compound is raloxifene. In certain embodiments, the compound is bazedoxifene. In certain embodiments, the compound is tamoxifen. In certain embodiments, the compound is etacstil. In certain embodiments, the compound is fulvestrant.

The term “pharmaceutically acceptable salt” refers to non-toxic pharmaceutically acceptable salts. See Gould, International Journal of Pharmaceutics 33: 201-217 (1986) and Berge et al., Journal of Pharmaceutical Sciences 66(1): 1-19 (1977). Other salts well known to those in the art may, however, be used. Representative organic or inorganic acids include, but are not limited to, hydrochloric, hydrobromic, hydriodic, perchloric, sulfuric, nitric, phosphoric, acetic, propionic, glycolic, lactic, succinic, maleic, fumaric, malic, tartaric, citric, benzoic, mandelic, methanesulfonic, hydroxyethanesulfonic, benzenesulfonic, oxalic, pamoic, 2-naphthalenesulfonic, p-toluenesulfonic, cyclohexanesulfamic, salicylic, saccharinic or trifluoroacetic acid. Representative organic or inorganic bases include, but are not limited to, basic or cationic salts such as benzathine, chloroprocaine, choline, diethanolamine, ethylenediamine, meglumine, procaine, aluminum, calcium, lithium, magnesium, potassium, sodium and zinc.

Embodiments also include prodrugs of the compounds disclosed herein. In general, such prodrugs will be functional derivatives of the compounds which are readily convertible in vivo into the required compound. Thus, in the methods of treatment of the present invention, the term “administering” shall encompass the treatment of the various disorders described with the compound specifically disclosed or with a compound which may not be specifically disclosed, but which converts to the specified compound in vivo after administration to the subject. Conventional procedures for the selection and preparation of suitable prodrug derivatives are described, for example, in “Design of Prodrugs”, H. Bundgaard, Elsevier, 1985.

Some of the crystalline forms for the compounds may exist as polymorphs and as such are intended to be included in the present invention. In addition, some of the compounds may form solvates with water (i.e., hydrates) or common organic solvents, and such solvates are intended to be encompassed by some embodiments.

Where the processes for the preparation of the compounds as disclosed herein give rise to mixtures of stereoisomers, these isomers may be separated by conventional techniques such as preparative chromatography. The compounds may be prepared in racemic form or as individual enantiomers or diastereomers by either stereospecific synthesis or by resolution. The compounds may, for example, be resolved into their component enantiomers or diastereomers by standard techniques, such as the formation of stereoisomeric pairs by salt formation with an optically active base, followed by fractional crystallization and regeneration of the free acid. The compounds may also be resolved by formation of stereoisomeric esters or amides, followed by chromatographic separation and removal of the chiral auxiliary. Alternatively, the compounds may be resolved using a chiral HPLC column. It is to be understood that all stereoisomers, racemic mixtures, diastereomers, cis-trans isomers, and enantiomers thereof are encompassed by some embodiments.

6.3. Pharmaceutical Compositions

Methods for treatment of estrogen receptor positive (ER⁺) cancers include administering a therapeutically effective amount of a compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant, a pharmaceutically acceptable salt thereof, or a prodrug thereof. The compound, the pharmaceutically acceptable salt, or the prodrug of the invention can be formulated in pharmaceutical compositions. In addition to the compound, the pharmaceutically acceptable salt thereof, or the prodrug thereof, the composition further comprises a pharmaceutically acceptable excipient, carrier, buffer, stabilizer or other materials well known to those skilled in the art. Such materials should be non-toxic and should not interfere with the efficacy of the active ingredient. The precise nature of the carrier or other material can depend on the route of administration, e.g. oral, intravenous, intramuscular, transdermal, vaginal topical, or vaginal ring.

Pharmaceutical compositions for oral administration can be in tablet, capsule, powder or liquid form. A tablet can include a solid carrier such as gelatin or an adjuvant. Liquid pharmaceutical compositions generally include a liquid carrier such as water, petroleum, animal oil, vegetable oil, mineral oil or synthetic oil. Physiological saline solution, dextrose or other saccharide solution or glycols such as ethylene glycol, propylene glycol or polyethylene glycol can also be included.

For parenteral administration, the compound will be in the form of a parenterally acceptable aqueous solution which is pyrogen-free and has suitable pH, isotonicity and stability. Those of relevant skill in the art are well able to prepare suitable solutions using, for example, isotonic vehicles such as Sodium Chloride Injection, Ringer's Injection, Lactated Ringer's Injection. Preservatives, stabilizers, buffers, antioxidants and/or other additives can be included, as required.

Pharmaceutical compositions for vaginal topical administration can be in the form of ointment, cream, gel or lotion. The pharmaceutical compositions for vaginal topical administration often include water, alcohol, animal oil, vegetable oil, mineral oil or synthetic oil. Hydrocarbon (paraffin), wool fat, beeswax, macrogols, emulsifying wax or cetrimide can also be included.

A composition can be administered alone or in combination with other treatments, either simultaneously or sequentially, dependent upon the condition to be treated.

6.4. Treatment Regimens

In the methods of administering an effective amount of a compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant in the form of a pharmaceutical composition as described above for treatment of ER⁺ cancer, the terms “treatment”, “treating”, and the like are used herein to generally mean obtaining a desired pharmacologic and/or physiologic effect. The effect may be prophylactic, in terms of completely or partially preventing a disease, condition, or symptoms thereof, and/or may be therapeutic in terms of a partial or complete cure for a disease or condition and/or adverse effect, such as a symptom, attributable to the disease or condition. “Treatment” as used herein covers any treatment of a disease or condition of a mammal, particularly a human, and includes: (a) preventing the disease or condition from occurring in a subject which may be predisposed to the disease or condition but has not yet been diagnosed as having it; (b) inhibiting the disease or condition (e.g., arresting its development); or (c) relieving the disease or condition (e.g., causing regression of the disease or condition, providing improvement in one or more symptoms). Improvements in any conditions can be readily assessed according to standard methods and techniques known in the art. The population of subjects treated by the method of the disease includes subjects suffering from the undesirable condition or disease, as well as subjects at risk for development of the condition or disease.

The term “effective amount” means a dose that produces the desired effect for which it is administered. The exact dose will depend on the purpose of the treatment, and will be ascertainable by one skilled in the art using known techniques. See Lloyd, The Art, Science and Technology of Pharmaceutical Compounding (1999).

6.4.1. Routes of Administration

In various embodiments, the compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant is administered by oral, intravenous, intramuscular, transdermal, vaginal topical, or vaginal ring administration.

In some embodiments, the compound is administered to the patient by oral administration. In certain embodiments, raloxifene is administered at about 10 mg/day per os to about 200 mg/day per os, such as about 20 mg/day per os to about 150 mg/day per os, about 30 mg/day per os to about 100 mg/day per os, or about 40 mg/day per os to about 80 mg/day per os. In particular embodiments, raloxifene is administered at about 10 mg/day per os, 20 mg/day per os, 40 mg/day per os, 60 mg/day per os, 80 mg/day per os, 100 mg/day per os, 120 mg/day per os, or 200 mg/day per os. In certain embodiments, bazedoxifene is administered at about 2 mg/day per os to about 100 mg/day per os, such as about 5 mg/day per os to about 80 mg/day per os, about 10 mg/day per os to about 50 mg/day per os, or about 20 mg/day per os to about 40 mg/day per os. In particular embodiments, bazedoxifene is administered at about 2 mg/day per os, 5 mg/day per os, 10 mg/day per os, 20 mg/day per os, 30 mg/day per os, 40 mg/day per os, 50 mg/day per os, or 100 mg/day per os. In certain embodiments, tamoxifen is administered at about 2 mg/day per os to about 100 mg/day per os, such as about 5 mg/day per os to about 80 mg/day per os, about 10 mg/day per os to about 50 mg/day per os, or about 20 mg/day per os to about 40 mg/day per os. In particular embodiments, tamoxifen is administered at about 2 mg/day per os, 5 mg/day per os, 10 mg/day per os, 20 mg/day per os, 30 mg/day per os, 40 mg/day per os, 50 mg/day per os, or 100 mg/day per os. In certain embodiments, the compound is administered once every day. In certain embodiments, the compound is administered once every two days. In certain embodiments, the compound is administered once every three days. In certain embodiments, the compound is administered once every four days. In certain embodiments, the compound is administered once every five days. In certain embodiments, the compound is administered once every six days. In certain embodiments, the compound is administered once every week. In certain embodiments, the compound is administered once every two weeks. In certain embodiments, the compound is administered once every three weeks. In certain embodiments, the compound is administered once every month.

In some embodiments, the compound is administered to the patient by intramuscular administration. In certain embodiments, fulvestrant is administered at about 100 mg to about 2000 mg, such as about 200 mg to about 1500 mg, about 400 mg to about 1000 mg, or about 500 mg to about 800 mg. In particular embodiments, bazedoxifene is administered at about 100 mg, 200 mg, 250 mg, 500 mg, 750 mg, 1000 mg, 1500 mg, or 2000 mg. In certain embodiments, the compound is administered once every day. In certain embodiments, the compound is administered once every two days. In certain embodiments, the compound is administered once every three days. In certain embodiments, the compound is administered once every four days. In certain embodiments, the compound is administered once every five days. In certain embodiments, the compound is administered once every six days. In certain embodiments, the compound is administered once every week. In certain embodiments, the compound is administered once every two weeks. In certain embodiments, the compound is administered once every three weeks. In certain embodiments, the compound is administered once every month.

In some embodiments, the compound is administered to ER⁺ cancer patient for one year. In some embodiments, the compound is administered to the patient for two years. In some embodiments, the compound is administered to the patient for three years. In some embodiments, the compound is administered to the patient for four years. In some embodiments, the compound is administered to the patient for five years. In some other embodiments, the compound is administered to the patient for more than five years. In certain embodiments, the compound is administered to the patient until the patient's cancer progresses on therapy.

6.4.2. Combination Therapy

In various embodiments, the compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant is administered either alone or in combination with other therapies. In certain embodiments, the compound is administered in combination with at least one other therapy. In some embodiments, the compound and other therapies are administered together (simultaneously). In some other embodiments, the compound and other therapies are administered at different times (sequentially).

In particular embodiments, the additional therapy that the patient is treated with is endocrine therapy. In various embodiments, the patient is treated with at least one line of additional endocrine therapy. In some embodiments, the patient is treated with one line of additional endocrine therapy. In some other embodiments, the patient is treated with multiple lines of additional endocrine therapy.

In some embodiments, the patient is treated with the additional endocrine therapy at the original doses. In some other embodiments, the patient is treated with the additional endocrine therapy at doses higher than original doses. In certain embodiments, the patient is treated with the additional endocrine therapy at doses lower than original doses.

In certain embodiments, the additional endocrine therapy is treatment with a selective ER modulator (SERM) other than the compound.

In certain embodiments, the additional endocrine therapy is treatment with a selective ER degrader (SERD) other than the compound.

In certain embodiments, the additional endocrine therapy is treatment with an aromatase inhibitor. In some of these embodiments, the aromatase inhibitor is selected from exemestane (Aromasin®), letrozole (Ferrara®), and anastrozole (Arimidex®).

In various embodiments, the additional therapy is administration to the patient of an effective amount of a cell cycle inhibitor. In certain embodiments, the additional therapy is administration of an effective amount of cyclin-dependent kinase 4/6 (CDK4/6) inhibitor. In some embodiments, the additional therapy is a CDK4/6 inhibitor selected from the group of palbociclib, abemaciclib, and ribociclib.

In some embodiments, the additional therapy is administration to the patient of an inhibitor of a pathway that cross-talks with and activates the ER transcriptional activity. In certain embodiments, the additional therapy is a mammalian target of rapamycin (mTOR) inhibitor. In specific embodiments, the mTOR inhibitor is Everolimus. In some of these embodiments, the compound in combination with Everolimus is administered to a postmenopausal woman with locally advanced or metastatic breast cancer who has progressed on a non-steroidal AI and/or fulvestrant either as monotherapy or in combination with a CDK4/6 inhibitor. In various embodiments, the additional therapy is a phosphoinositide 3-kinase (PI3K) inhibitor or a heat shock protein 90 (HSP90) inhibitor.

In various embodiments, the additional therapy is administration to the patient of an effective amount of a growth factor inhibitor. In certain embodiments, the additional therapy is a human epidermal growth factor receptor 2 (HER2) inhibitor. In some embodiments, the HER2 inhibitor is trastuzumab (Herceptin®). In some other embodiments, the HER2 inhibitor is ado-trastuzumab emtansine (Kadcyla®).

In some embodiments, the additional therapy is administering to the patient an effective amount of a histone deacetylase (HDAC) inhibitor. In various embodiments, the HDAC inhibitor is vorinostat (Zolinza®), romidepsin (Istodax®), chidamide (Epidaza®), panobinostat (Farydak®), belinostat (Beleodaq®, PXD101), valproic acid (Depakote®, Depakene®, Stavzor®), mocetinostat (MGCD0103), abexinostat (PCI-24781), entinostat (MS-275), pracinostat (SB939), resminostat (4SC-201), givinostat (ITF2357), quisinostat (JNJ-26481585), kevetrin, CUDC-101, AR-42, tefinostat (CHR-2835), CHR-3996, 4SC202, CG200745, rocilinostat (ACY-1215), or sulforaphane. In certain embodiments, the HDAC inhibitor is entinostat (MS-275). In certain other embodiments, the HDAC inhibitor is vorinostat (Zolinza®). In yet certain other embodiments, the HDAC inhibitor is romidepsin (Istodax®).

In some embodiments, the additional therapy is administering to the patient an effective amount of a checkpoint inhibitor. In certain embodiments, the checkpoint inhibitor is an antibody. In some of these embodiments, the checkpoint inhibitor is an antibody specific for programmed cell death protein 1 (PD-1), programmed death-ligand 1 (PD-L1), or cytotoxic T-lymphocyte-associated protein 4 (CTLA-4). In some embodiments, the PD-1 antibody is pembrolizumab (Keytruda®) or nivolumab (Opdivo®). In some embodiments, the CTLA-4 antibody is ipilimumab (Yervo®).

In certain embodiments, the additional therapy is administering to the patient an effective amount of cancer vaccine.

In some embodiments, the additional therapy is administering to the patient an effective amount of denosumab.

In some embodiments, the additional therapy is administering to the patient an effective amount of a serotonin-norepinephrine reuptake inhibitor (SNRI), a selective serotonin reuptake inhibitor (SSRI), or gabapentin. In certain embodiments, the SNRI is venlafaxine (Effexor®).

6.4.3. Clinical Endpoints

6.4.3.1. Primary Clinical Endpoints

In various embodiments, the method comprises administering an amount of a compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant effective to increase the disease-free survival of the ER⁺ cancer patient. In some embodiments, the method comprises administering an amount of a compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant in an amount effective to reduce recurrence of ER⁺ cancer. In some embodiments, the method comprises administering an amount of a compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant in an amount effective to increase time to recurrence of ER⁺ cancer. In some embodiments, the method comprises administering an amount of a compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant in an amount effective to reduce metastasis of ER⁺ cancer. In some embodiments, the method comprises administering an amount of a compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant in an amount effective to increase duration of progression-free survival of the ER⁺ cancer patient.

In various embodiments, the method increases the disease-free survival of the ER⁺ breast cancer patient. In certain embodiments, the method reduces recurrence of ER⁺ breast cancer. In certain embodiments, the method increases time to recurrence of ER⁺ breast cancer. In certain embodiments, the method reduces metastasis of ER⁺ breast cancer to bone. In certain embodiments, the method reduces metastasis of ER⁺ breast cancer to tissues other than bone. In certain embodiments, the method increases duration of progression-free survival of the ER⁺ breast cancer patient.

In various embodiments, the method increases the disease-free survival in ER⁺ cancer patient with endocrine resistance. In some embodiments, the method reduces recurrence of cancer in patient with endocrine resistance. In some embodiments, the method increases time to recurrence of cancer in patient with endocrine resistance. In some embodiments, the method reduces metastasis of cancer in patient with endocrine resistance. In some embodiments, the method increases duration of progression-free survival in ER⁺ cancer patient with endocrine resistance.

In some preferred embodiments, the method increases disease-free survival, reduces recurrence, increases time to recurrence, reduces metastasis, and/or increases duration of progression-free survival in patients with ER⁺ locally advanced or metastatic breast cancer that has developed endocrine resistance. In particular embodiments, the breast cancer has developed endocrine resistance by acquiring one or more of the ESR1 mutations discussed herein. In some embodiments, the method reduces the selective pressure and prevents the expansion of the endocrine resistant clones in ER⁺ locally advanced or metastatic breast cancer during treatment.

6.4.3.2. Secondary Clinical Endpoints

In some embodiments, the method is effective to prevent fracture and bone loss in women who are concurrently being treated with one or more drugs causing or predisposing to osteoporosis.

In some embodiments, the method is effective to decrease vaginal pH, increase vaginal lubrication, and/or improve vaginal cell maturation index in women who are concurrently being treated with one or more drugs causing or predisposing to vulvovaginal atrophy (VVA).

In some embodiments, the method reduces one or more symptoms of sexual dysfunction in women who are concurrently being treated with one or more drugs causing or predisposing to sexual dysfunction.

In some embodiments, the method treats hot flashes in women who are concurrently being treated with one or more drugs causing or predisposing to hot flashes.

In some embodiments, the method increases one or more quality of life measures selected from joint ache, urogenital symptoms, bone loss, and bone fractures.

6.5. EXAMPLES

Below are examples of specific embodiments for carrying out the present invention. The examples are offered for illustrative purposes only, and are not intended to limit the scope of the present invention in any way. Efforts have been made to ensure accuracy with respect to numbers used (e.g., amounts, temperatures, etc.), but some experimental error and deviation should, of course, be allowed for.

The practice of the present invention will employ, unless otherwise indicated, conventional methods of molecular biology, cell biology, biochemistry, genetics, cancer biology, and pharmacology, within the skill of the art. Such techniques are explained fully in the literature.

6.5.1. Example 1 Efficacy of Raloxifene, Bazedoxifene, Tamoxifen, Etacstil, and Fulvestrant on ESR1 LBD Mutations

6.5.1.1. Methods

6.5.1.1.1. Site-Directed Mutagenesis

ExSite mutagenesis was performed using the corresponding primers as summarized in Table 1 below on a pENTR2B ERα WT construct using Pfu ultra taq polymerase. The primers were PNK phosphorylated. Following PCR amplification, the products were digested with DpnI at 37° C. for 1 hr, followed by overnight ligation at 16° C. Ligated products were transformed into DH5α bacterial cells and grown on kanamycin resistant plates. The pENTR clones were verified by sequencing and then swapped into the pcDNA-DEST vector using the Gateway system (Invitrogen) for expression analysis.

TABLE 1  Primers for Mutagenesis ER Y537N For AATGACCTGCTGCTGGAGATG SEQ ID NO: 1 ER Y537N Rev GAGGGGCACCACGTTCTTGCA SEQ ID NO: 2 ER Y537S For GACCTGCTGCTGGAGATGCTG SEQ ID NO: 3 ER Y537S Rev GCTGAGGGGCACCACGTTCTT SEQ ID NO: 4 ER Y537C For TGTGACCTGCTGCTGGAGATG SEQ ID NO: 5 ER Y537C Rev GCTGAGGGGCACCACGTTCTT SEQ ID NO: 6 ER D538G For GGTCTGCTGCTGGAGATGCTG SEQ ID NO: 7 ER D538G Rev ATAGAGGGGCACCACGTTCTT SEQ ID NO: 8

6.5.1.1.2. Cell Culture

Caov2 ovarian carcinoma cells were grown in RPMI-1640 media (Gibco) supplemented with 8% Fetal Bovine Serum (FBS), Sodium Pyruvate (NaPyr) and non-essential amino acids (NEAA) and passaged every 2-3 days. SKBR3 breast adenocarcinoma cells were grown in DMEM media (Gibco) supplemented with 8% Fetal Bovine Serum (FBS), Sodium Pyruvate (NaPyr) and non-essential amino acids (NEAA) and passaged every 2-3 days. Cells were switched into a phenol-red free RPMI-1640 media supplemented with 8% charcoal stripped fetal bovine serum (CFS), NaPyr, and NEAA one day before plating for experiment. Cells were then plated in 96-well plates for experiment in the phenol red-free media an additional day before transfection.

6.5.1.1.3. Reporter Gene Assay

Caov2 cells were co-transfected with the 7X-TK-ERE-TATA luciferase reporter gene (Nagel et al., Endocrinology 142(11): 4721-4728 (2001)) and expression constructs for either wild-type or mutant receptors using Fugene transfection reagent (Promega). SKBR3 cells were co-transfected with 3X-TK-ERE-TATA luciferase reporter gene in the same conditions. pCMV-β-gal was used as a control for transfection efficiency and pcDNA was added for a final DNA concentration of 75 ng per triplicate group. Cells were treated with indicated ligand five hours post transfection. Following 24 hours of treatment, cells were lysed and the luciferase and β-gal assays were performed as described previously (Norris et al., J Biol Chem 270(39): 22777-22782 (1995)) and the plates were read on the Fusion α-FP HT plate reader (PerkinElmer Life Sciences).

6.5.1.2. Results

ERα expression constructs were engineered to express one of four different ESR1 LBD mutations, Y537S, Y537N, Y537C, and D538G, which are found in metastatic breast cancer patients. See Jeselsohn et al., Nature Reviews Clinical Oncology 12(10): 573-583 (2015); Jeselsohn et al., Clinical Cancer Research 20(7): 1757-1767 (2014); Robinson et al., Nature Genetics 45(12): 1446-1451(2013); Thomas and Gustafsson, Trends in Endocrinology and Metabolism 26(9): 467-476 (2015); and Toy et al., Nature Genetics 45(12): 1439-1445 (2013). The activity of these mutants was evaluated in a reconstituted estrogen response element (ERE)-luciferase reporter assay in Caov2 ovarian carcinoma cells and SKBR3 breast adenocarcinoma cells. Data normalization is done in respect to the “0” data point (no ligand) of the wild-type receptor. As previously reported (Jeselsohn et al., 2014; Robinson et al., 2013; Toy et al., 2013), all of the mutants studied exhibited substantial constitutive activity when compared to the activity of wild-type (WT) ERα in the absence of its ligand: 17-β estradiol (E2). While the WT ERα responds to E2 in a dose-response matter, the transcriptional activity of the mutants is not responsive to E2 activation (FIG. 1A and FIG. 3A).

The ability of raloxifene, bazedoxifene, 4-hydroxytamoxifen (4OHT), 4-hydroxy metabolite of etacstil (GW-7604), and fulvestrant (ICI) to inhibit the transcriptional activity of the ERα mutants was next evaluated under the same conditions. All inhibition curves were done in the presence of 10⁻⁹ (1 nM) 17-β estradiol. Data normalization was done in respect to the “0” data point (no raloxifene, bazedoxifene, 4-hydroxytamoxifen (4OHT), 4-hydroxy metabolite of etacstil (GW-7604), or fulvestrant (ICI)) for each individual receptor. The plots include data from five independent experiments and each value is an average of triplicates from each experiment. Notably, raloxifene, bazedoxifene, 4-hydroxytamoxifen (4OHT), 4-hydroxy metabolite of etacstil (GW-7604), and fulvestrant (ICI) each effectively inhibited the transcriptional activity of all tested ERα LBD mutants in a dose-response manner (FIGS. 1C-1F, FIGS. 3C-3F, FIGS. 4A-4E, and FIGS. 2A-2E).

The transcriptional IC90 values of ER modulators were also evaluated under the same conditions in Caov2 ovarian carcinoma cells and SKBR3 breast adenocarcinoma cells. The tests included raloxifene, bazedoxifene, 4-hydroxytamoxifen (4OHT), 4-hydroxy metabolite of etacstil (GW-7604), and fulvestrant (ICI) individually. See Maximov et al., Current Clinical Pharmacology 8(2): 135-155 (2013) and McDonnell et al., Journal of Medicinal Chemistry 58(12): 4883-4887 (2015). The transcriptional IC90 values of ER modulators evaluated were compared to the Cmax of these compounds in blood at approved doses. See Highlights of Prescribing Information: Evista, 2007; Highlights of Prescribing Information: Faslodex, 2012; Nolvadex, 2006; and Summary of Product Characteristics: Conbriza 2009. The results from Caov2 ovarian carcinoma cells and SKBR3 breast adenocarcinoma cells are summarized in Table 2.

TABLE 2 Comparison of IC90 Values to Reported Cmax Values Caov2 SKBR3 Reported Converted (M) Caov2 Ratio SKBR3 Ratio Compound Cmax Cmax IC90 Cmax/IC90 IC90 Cmax/IC90 WT ICI (500 mg) 28 ng/mL 4.60E−08 4.76E−12 9654.54 1.10E−08 4.18 4OHT (20 mg) 40 ng/mL 1.10E−07 9.24E−10 119.01 3.20E−09 34.38 Raloxifene (60 mg) 1.36 ng/mL   2.87E−09 1.19E−10 24.03 1.20E−09 2.39 Bazedoxifene (20 mg) 6.2 ng/mL  7.29E−09 1.68E−11 433.85 6.00E−09 1.22 GW 7604 NR NR 7.72E−08 NA 2.10E−07 NA Y537N ICI (500 mg) 28 ng/mL 4.60E−08 7.48E−09 6.15 3.40E−07 0.14 4OHT (20 mg) 40 ng/mL 1.10E−07 9.45E−09 11.6 1.30E−07 0.85 Raloxifene (60 mg) 1.36 ng/mL   2.87E−09 4.23E−10 6.79 9.00E−09 0.32 Bazedoxifene (20 mg) 6.2 ng/mL  7.29E−09 2.41E−09 3.02 3.50E−08 0.21 GW 7604 NR NR 3.45E−07 NA 1.70E−07 NA Y537S ICI (500 mg) 28 ng/mL 4.60E−08 8.65E−08 0.53 7.70E−08 0.6 4OHT (20 mg) 40 ng/mL 1.10E−07 7.99E−08 1.38 2.60E−08 4.23 Raloxifene (60 mg) 1.36 ng/mL   2.87E−09 6.27E−09 0.46 5.00E−09 0.57 Bazedoxifene (20 mg) 6.2 ng/mL  7.29E−09 4.09E−08 0.18 6.90E−09 1.06 GW 7604 NR NR 1.97E−06 NA 2.50E−06 NA Y537C ICI (500 mg) 28 ng/mL 4.60E−08 7.99E−09 5.76 3.30E−08 1.39 4OHT (20 mg) 40 ng/mL 1.10E−07 8.31E−09 13.24 5.90E−08 1.86 Raloxifene (60 mg) 1.36 ng/mL   2.87E−09 1.09E−09 2.62 8.90E−09 0.32 Bazedoxifene (20 mg) 6.2 ng/mL  7.29E−09 1.49E−09 4.88 8.60E−09 0.85 GW 7604 NR NR 2.00E−07 NA 3.60E−07 NA D538G ICI (500 mg) 28 ng/mL 4.60E−08 7.29E−08 0.63 1.40E−07 0.33 4OHT (20 mg) 40 ng/mL 1.10E−07 3.95E−08 2.78 1.90E−07 0.58 Raloxifene (60 mg) 1.36 ng/mL   2.87E−09 4.39E−09 0.65 1.40E−08 0.21 Bazedoxifene (20 mg) 6.2 ng/mL  7.29E−09 2.07E−08 0.35 2.00E−08 0.36 GW 7604 NR NR 7.82E−07 NA 4.50E−07 NA

As expected, the WT receptor was the most responsive to anti-estrogen treatment, with each of the mutants exhibiting reduced response to the inhibitory actions of these compounds. Importantly, the pharmacology of each of the mutants was different, which highlights the need to match patients with the most appropriate drug. The data suggest that raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant (ICI) are each effective for patients whose tumors express the ESR1 LBD mutations in both ovarian and breast cancer settings.

6.5.2. Example 2 Efficacy of Tamoxifen and Fulvestrant on ESR1 LBD Mutations Y537S and D538G in Stable Transfectants

MCF7 estrogen receptor alpha positive (ER⁺) breast cancer cells were engineered to stably express doxycycline (DOX)-inducible hemagglutinin (HA)-tagged full length ER with ligand binding domain mutations Y537S and D538G. The introduction and expression of the mutants were confirmed by Sanger sequencing, RNA-sequencing, and western blot.

The dose response studies were performed in full medium conditions. Cells were treated with DOX for the induction of HA-tagged mutated ER or with vehicle as control, and plated in triplicate. Subsequently, on day 5, cell counting was performed using the Celigo instrument with Hoechst dye staining to detect nucleated live cells and propidium iodide to quantify dead cells. Treatments included vehicle and increasing doses of 4-hydroxytamoxifen (4OHT) and fulvestrant starting from 10⁻¹² M with 10 fold increments up to 10⁻⁶ M. The efficacy of the treatment is inversely proportional to the cell count.

The anti-estrogenic activity of 4-hydroxytamoxifen (4OHT) and fulvestrant in a breast cancer model of ER mutations Y537S and D538G identified in Example 1 was confirmed by the ability of 4-hydroxytamoxifen (4OHT) and fulvestrant to overcome resistance with increasing dose titration and kill the stably transfected cells, respectively.

IC50 values were calculated using PRISM for 4-hydroxytamoxifen (4OHT) and fulvestrant. The results are summarized in Table 3.

TABLE 3 Comparison of IC50 Values in the Absence and the Presence of DOX DOX No DOX (ESR Treatment Allele (wt only) mutation) Fold Change 4OHT Y537S 4.7E−10 2.1E−9 4.47 4OHT D538G 2.8E−10 5.7E−10 2 Fulvestrant Y537S 1.9E−10   5E−10 2.6 Fulvestrant D538G 2.5E−10 1.8E−9 7.2

The results confirmed that tamoxifen treatment and fulvestrant treatment each is effective on the Y537S and D538G mutations, although the Y537S and D538G mutations require higher concentrations to overcome resistance.

7. EQUIVALENTS AND INCORPORATION BY REFERENCE

While the invention has been particularly shown and described with reference to a preferred embodiment and various alternate embodiments, it will be understood by persons skilled in the relevant art that various changes in form and details can be made therein without departing from the spirit and scope of the invention.

All references, issued patents and patent applications cited within the body of the instant specification are hereby incorporated by reference in their entirety, for all purposes. 

1. A method of treating locally advanced or metastatic breast cancer in women, comprising: a) selecting for treatment a patient who has been diagnosed with estrogen receptor positive (ER⁺) locally advanced or metastatic breast cancer; and b) administering to the selected patient an effective amount of a compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant, a pharmaceutically acceptable salt thereof, or a prodrug thereof, wherein the patient's cancer has at least one gain of function missense mutation within the ligand binding domain (LBD) of the Estrogen Receptor 1 (ESR1) gene.
 2. The method of claim 1, wherein the patient has previously been determined to have at least one gain of function missense mutation within the ligand binding domain (LBD) of the Estrogen Receptor 1 (ESR1) gene.
 3. The method of claim 1, further comprising the earlier step of: determining that the patient has at least one gain of function missense mutation within the ligand binding domain (LBD) of the Estrogen Receptor 1 (ESR1) gene.
 4. The method of any one of claims 1 to 3, wherein the at least one of gain of function missense mutation is in any one of amino acids D538, Y537, L536, P535, V534, S463, V392, and E380.
 5. The method of claim 4, wherein the at least one gain of function missense mutation is in the amino acid D538.
 6. The method of claim 5, wherein the mutation is D538G.
 7. The method of claim 4, wherein the at least one gain of function missense mutation is in the amino acid Y537.
 8. The method of claim 7, wherein the mutation is Y537S, Y537N, Y537C, or Y537Q.
 9. The method of claim 8, wherein the mutation is Y537C.
 10. The method of claim 4, wherein the at least one gain of function missense mutation is in the amino acid L536.
 11. The method of claim 10, wherein the mutation is L536R or L536Q.
 12. The method of claim 4, wherein the at least one gain of function missense mutation is in the amino acid P535.
 13. The method of claim 12, wherein the mutation is P535H.
 14. The method of claim 4, wherein the mutation is in the at least one gain of function missense amino acid V534.
 15. The method of claim 14, wherein the mutation is V534E.
 16. The method of claim 4, wherein the at least one gain of function missense mutation is in the amino acid S463.
 17. The method of claim 16, wherein the mutation is S463P.
 18. The method of claim 4, wherein the at least one gain of function missense mutation is in the amino acid V392.
 19. The method of claim 18, wherein the mutation is V392I.
 20. The method of claim 4, wherein the at least one gain of function missense mutation is in the amino acid E380.
 21. The method of claim 20, wherein the mutation is E380Q.
 22. The method of any one of claims 1 to 21, wherein the serum estradiol level of the patient is at least 0.35 ng/dL.
 23. The method of any one of claims 1 to 21, wherein the serum estradiol level of the patient is about 0.30 ng/dL to about 0.35 ng/dL.
 24. The method of any one of claims 1 to 21, wherein the serum estradiol level of the patient is about 0.25 ng/dL to about 0.30 ng/dL.
 25. The method of any one of claims 1 to 24, wherein the compound is administered by oral, intravenous, transdermal, vaginal topical, or vaginal ring administration.
 26. The method of any one of claims 1 to 25, wherein the compound is administered once every day, once every two days, once every three days, once every four days, once every five days, once every six days, once every week, once every two weeks, once every three weeks, or once every month.
 27. The method of any one of claims 1 to 26, further comprising treating said patient with at least one additional endocrine therapy.
 28. The method of claim 27, wherein said patient is treated with the additional endocrine therapy at original doses.
 29. The method of claim 27, wherein said patient is treated with the additional endocrine therapy at doses higher than original doses.
 30. The method of any one of claims 27 to 29, wherein the additional endocrine therapy is treatment with lasofoxifene.
 31. The method of any one of claims 27 to 29, wherein the additional endocrine therapy is treatment with an aromatase inhibitor.
 32. The method of any one of claims 1 to 26, further comprising administering to said patient an effective amount of cyclin-dependent kinase 4/6 (CDK4/6) inhibitor.
 33. The method of claim 32, wherein said CDK4/6 inhibitor is palbociclib, abemaciclib, or ribociclib.
 34. The method of any one of claims 1 to 26, further comprising administering to said patient an effective amount of mammalian target of rapamycin (mTOR) inhibitor.
 35. The method of claim 34, wherein said mTOR inhibitor is Everolimus.
 36. The method of any one of claims 1 to 26, further comprising administering to said patient an effective amount of phosphoinositide 3-kinase (PI3K) inhibitor or heat shock protein 90 (HSP90) inhibitor.
 37. The method of any one of claims 1 to 26, further comprising administering to said patient an effective amount of human epidermal growth factor receptor 2 (HER2) inhibitor.
 38. The method of claim 37, wherein said HER2 inhibitor is trastuzumab (Herceptin®) or ado-trastuzumab emtansine (Kadcyla®).
 39. The method of any one of claims 1 to 26, further comprising administering to said patient an effective amount of a histone deacetylase (HDAC) inhibitor.
 40. The method of claim 39, wherein said HDAC inhibitor is vorinostat (Zolinza®), romidepsin (Istodax®), chidamide (Epidaza®), panobinostat (Farydak®), belinostat (Beleodaq®, PXD101), valproic acid (Depakote®, Depakene®, Stavzor®), mocetinostat (MGCD0103), abexinostat (PCI-24781), entinostat (MS-275), pracinostat (SB939), resminostat (4SC-201), givinostat (ITF2357), quisinostat (JNJ-26481585), kevetrin, CUDC-101, AR-42, tefinostat (CHR-2835), CHR-3996, 4SC202, CG200745, rocilinostat (ACY-1215), or sulforaphane.
 41. The method of any one of claims 1 to 26, further comprising administering to said patient an effective amount of a checkpoint inhibitor.
 42. The method of claim 41, wherein said checkpoint inhibitor is an antibody specific for programmed cell death protein 1 (PD-1), programmed death-ligand 1 (PD-L1), or cytotoxic T-lymphocyte-associated protein 4 (CTLA-4).
 43. The method of claim 42, wherein said PD-1 antibody is pembrolizumab (Keytruda®) or nivolumab (Opdivo®).
 44. The method of claim 42, wherein said CTLA-4 antibody is ipilimumab (Yervoy®).
 45. The method of any one of claims 1 to 26, further comprising administering to said patient an effective amount of cancer vaccine.
 46. The method of any one of claims 1 to 45, wherein the patient is premenopausal.
 47. The method of claim 46, wherein the patient has locally advanced or metastatic ER+/HER2− breast cancer.
 48. The method of claim 47, wherein the patient has progressed on her first hormonal treatment while on a non-steroid aromatase inhibitor (AI), fulvestrant, AI in combination with a CDK4/6 inhibitor, or fulvestrant in combination with a CDK4/6 inhibitor.
 49. The method of any one of claims 1 to 45, wherein the patient is perimenopausal.
 50. The method of claim 49, wherein the patient has locally advanced or metastatic ER+/HER2− breast cancer.
 51. The method of claim 50, wherein the patient has progressed on her first hormonal treatment while on a non-steroid aromatase inhibitor (AI), fulvestrant, AI in combination with a CDK4/6 inhibitor, or fulvestrant in combination with a CDK4/6 inhibitor.
 52. The method of any one of claims 1 to 45, wherein the patient is postmenopausal.
 53. The method of claim 52, wherein the patient has locally advanced or metastatic ER+/HER2− breast cancer.
 54. The method of claim 53, wherein the patient has progressed on her first hormonal treatment while on a non-steroid aromatase inhibitor (AI), fulvestrant, AI in combination with a CDK4/6 inhibitor, or fulvestrant in combination with a CDK4/6 inhibitor.
 55. A method of treating a female patient suffering from breast cancer who is at risk of acquiring at least one gain of function missense mutation within the ligand binding domain (LBD) of the Estrogen Receptor 1 (ESR1) gene, comprising administering to the female patient an effective amount of a compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant, a pharmaceutically acceptable salt thereof, or a prodrug thereof.
 56. The method of claim 55, wherein the patient is at risk of acquiring resistance to endocrine therapy, optionally wherein the endocrine therapy is (i) selective ER modulator (SERM) therapy, (ii) selective ER degrader (SERD) therapy, (iii) aromatase inhibitor (AI) therapy, or (iv) any combination of (i), (ii) and/or (iii).
 57. The method of claim 55 or claim 56, wherein the patient has primary breast cancer.
 58. The method of claim 57, wherein the primary breast cancer is locally advanced.
 59. The method of any one of claims 55 to 58, wherein the patient has been treated with endocrine therapy, optionally wherein the endocrine therapy is (i) selective ER modulator (SERM) therapy, (ii) selective ER degrader (SERD) therapy, (iii) aromatase inhibitor (AI) therapy, or (iv) any combination of (i), (ii) and/or (iii).
 60. A method of treating a female patient suffering from estrogen receptor positive (ER⁺) primary breast cancer, comprising administering to a female patient an effective amount of a compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant, a pharmaceutically acceptable salt thereof, or a prodrug thereof, wherein the patient has cancer cells with at least one gain of function missense mutation within the ligand binding domain (LBD) of the Estrogen Receptor 1 (ESR1) gene.
 61. The method of claim 60, wherein the patient is at risk of acquiring resistance to endocrine therapy, optionally wherein the endocrine therapy is (i) selective ER modulator (SERM) therapy, (ii) selective ER degrader (SERD) therapy, (iii) aromatase inhibitor (AI) therapy, or (iv) any combination of (i), (ii) and/or (iii).
 62. The method of claim 60 or claim 61, wherein the primary breast cancer is locally advanced.
 63. The method of any one of claims 60 to 62, wherein the patient has been treated with endocrine therapy, optionally wherein the endocrine therapy is (i) selective ER modulator (SERM) therapy, (ii) selective ER degrader (SERD) therapy, (iii) aromatase inhibitor (AI) therapy, or (iv) any combination of (i), (ii) and/or (iii).
 64. A method of treating a female patient suffering from estrogen receptor positive (ER⁺) locally advanced or metastatic breast cancer, comprising administering to a female patient an effective amount of a compound selected from the group consisting of raloxifene, bazedoxifene, tamoxifen, etacstil, and fulvestrant, a pharmaceutically acceptable salt thereof, or a prodrug thereof, wherein the patient has cancer cells with at least one gain of function missense mutation within the ligand binding domain (LBD) of the Estrogen Receptor 1 (ESR1) gene.
 65. The method of claims 55 to 64, wherein the at least one of gain of function missense mutation is in any one of amino acids D538, Y537, L536, P535, V534, S463, V392, and E380.
 66. The method of claim 65, wherein the at least one gain of function missense mutation is in the amino acid D538.
 67. The method of claim 66, wherein the mutation is D538G.
 68. The method of claim 65, wherein the at least one gain of function missense mutation is in the amino acid Y537.
 69. The method of claim 68, wherein the mutation is Y537S, Y537N, Y537C, or Y537Q.
 70. The method of claim 69, wherein the mutation is Y537C.
 71. The method of claim 65, wherein the at least one gain of function missense mutation is in the amino acid L536.
 72. The method of claim 71, wherein the mutation is L536R or L536Q.
 73. The method of claim 65, wherein the at least one gain of function missense mutation is in the amino acid P535.
 74. The method of claim 73, wherein the mutation is P535H.
 75. The method of claim 65, wherein the at least one gain of function missense mutation is in the amino acid V534.
 76. The method of claim 75, wherein the mutation is V534E.
 77. The method of claim 65, wherein the at least one gain of function missense mutation is in the amino acid
 5463. 78. The method of claim 77, wherein the mutation is S463P.
 79. The method of claim 65, wherein the at least one gain of function missense mutation is in the amino acid V392.
 80. The method of claim 79, wherein the mutation is V392I.
 81. The method of claim 65, wherein the at least one gain of function missense mutation is in the amino acid E380.
 82. The method of claim 81, wherein the mutation is E380Q.
 83. The method of any one of claims 55 to 82, wherein the compound is administered by oral, intravenous, transdermal, vaginal topical, or vaginal ring administration.
 84. The method of any one of claims 55 to 83, wherein the compound is administered once every day, once every two days, once every three days, once every four days, once every five days, once every six days, once every week, once every two weeks, once every three weeks, or once every month.
 85. The method of any one of claims 55 to 84, further comprising treating said patient with at least one additional endocrine therapy.
 86. The method of claim 85, wherein said patient is treated with the additional endocrine therapy at original doses.
 87. The method of claim 85, wherein said patient is treated with the additional endocrine therapy at doses higher than original doses.
 88. The method of any one of claims 85 to 87, wherein the additional endocrine therapy is treatment with lasofoxifene.
 89. The method of any one of claims 85 to 87, wherein the additional endocrine therapy is treatment with an aromatase inhibitor.
 90. The method of any one of claims 55 to 84, further comprising administering to said patient an effective amount of cyclin-dependent kinase 4/6 (CDK4/6) inhibitor.
 91. The method of claim 90, wherein said CDK4/6 inhibitor is palbociclib, abemaciclib, or ribociclib.
 92. The method of any one of claims 55 to 84, further comprising administering to said patient an effective amount of mammalian target of rapamycin (mTOR) inhibitor.
 93. The method of claim 92, wherein said mTOR inhibitor is Everolimus.
 94. The method of any one of claims 55 to 84, further comprising administering to said patient an effective amount of phosphoinositide 3-kinase (PI3K) inhibitor or heat shock protein 90 (HSP90) inhibitor.
 95. The method of any one of claims 55 to 84, further comprising administering to said patient an effective amount of human epidermal growth factor receptor 2 (HER2) inhibitor.
 96. The method of claim 95, wherein said HER2 inhibitor is trastuzumab (Herceptin®) or ado-trastuzumab emtansine (Kadcyla®).
 97. The method of any one of claims 55 to 84, further comprising administering to said patient an effective amount of a histone deacetylase (HDAC) inhibitor.
 98. The method of claim 97, wherein said HDAC inhibitor is vorinostat (Zolinza®), romidepsin (Istodax®), chidamide (Epidaza®), panobinostat (Farydak®), belinostat (Beleodaq®, PXD101), valproic acid (Depakote®, Depakene®, Stavzor®), mocetinostat (MGCD0103), abexinostat (PCI-24781), entinostat (MS-275), pracinostat (SB939), resminostat (4SC-201), givinostat (ITF2357), quisinostat (JNJ-26481585), kevetrin, CUDC-101, AR-42, tefinostat (CHR-2835), CHR-3996, 4SC202, CG200745, rocilinostat (ACY-1215), or sulforaphane.
 99. The method of any one of claims 55 to 84, further comprising administering to said patient an effective amount of a checkpoint inhibitor.
 100. The method of claim 99, wherein said checkpoint inhibitor is an antibody specific for programmed cell death protein 1 (PD-1), programmed death-ligand 1 (PD-L1), or cytotoxic T-lymphocyte-associated protein 4 (CTLA-4).
 101. The method of claim 100, wherein said PD-1 antibody is pembrolizumab (Keytruda®) or nivolumab (Opdivo®).
 102. The method of claim 100, wherein said CTLA-4 antibody is ipilimumab (Yervoy®).
 103. The method of any one of claims 55 to 84, further comprising administering to said patient an effective amount of cancer vaccine.
 104. The method of any one of claims 55 to 103, wherein the patient is premenopausal.
 105. The method of claim 104, wherein the patient has locally advanced or metastatic ER+/HER2− breast cancer.
 106. The method of claim 105, wherein the patient has progressed on her first hormonal treatment while on a non-steroid aromatase inhibitor (AI), fulvestrant, AI in combination with a CDK4/6 inhibitor, or fulvestrant in combination with a CDK4/6 inhibitor.
 107. The method of any one of claims 55 to 103, wherein the patient is perimenopausal.
 108. The method of claim 107, wherein the patient has locally advanced or metastatic ER+/HER2− breast cancer.
 109. The method of claim 108, wherein the patient has progressed on her first hormonal treatment while on a non-steroid aromatase inhibitor (AI), fulvestrant, AI in combination with a CDK4/6 inhibitor, or fulvestrant in combination with a CDK4/6 inhibitor.
 110. The method of any one of claims 55 to 103, wherein the patient is postmenopausal.
 111. The method of claim 110, wherein the patient has locally advanced or metastatic ER+/HER2− breast cancer.
 112. The method of claim 111, wherein the patient has progressed on her first hormonal treatment while on a non-steroid aromatase inhibitor (AI), fulvestrant, AI in combination with a CDK4/6 inhibitor, or fulvestrant in combination with a CDK4/6 inhibitor. 